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Amandine PERRIN
panacota
Commits
a524547a
Commit
a524547a
authored
4 years ago
by
Amandine PERRIN
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publish singularity image for version 1.0
parent
b20afeed
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Pipeline
#36748
passed
4 years ago
Stage: test
Stage: coverage
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PanACoTA/__init__.py
+1
-1
1 addition, 1 deletion
PanACoTA/__init__.py
containers/Singularity
+8
-15
8 additions, 15 deletions
containers/Singularity
with
9 additions
and
16 deletions
PanACoTA/__init__.py
+
1
−
1
View file @
a524547a
"""
PanACoTA
"""
"""
PanACoTA
"""
__version__
=
20190425
__version__
=
1.0
This diff is collapsed.
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containers/
panacota-s
ingularity
.def
→
containers/
S
ingularity
+
8
−
15
View file @
a524547a
...
@@ -14,10 +14,6 @@ From:python:3.7-stretch
...
@@ -14,10 +14,6 @@ From:python:3.7-stretch
# Install packages needed
# Install packages needed
apt-get install -y wget
apt-get install -y wget
# apt-get install -y \
# wget \
# python3 \
# python3-pip
# Upgrade pip
# Upgrade pip
pip3 install --upgrade pip
pip3 install --upgrade pip
...
@@ -25,14 +21,6 @@ From:python:3.7-stretch
...
@@ -25,14 +21,6 @@ From:python:3.7-stretch
# For manually-installed programs
# For manually-installed programs
mkdir -p /opt/src
mkdir -p /opt/src
# Update makeblastdb and blastp for prokka
cd /opt/src
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install mash
# Install mash
cd /opt/src
cd /opt/src
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
...
@@ -40,7 +28,14 @@ From:python:3.7-stretch
...
@@ -40,7 +28,14 @@ From:python:3.7-stretch
rm mash-Linux64-v2.2.tar &&\
rm mash-Linux64-v2.2.tar &&\
mv /opt/src/mash-Linux64-v2.2/mash /usr/local/bin &&\
mv /opt/src/mash-Linux64-v2.2/mash /usr/local/bin &&\
rm -r mash-Linux64-v2.2
rm -r mash-Linux64-v2.2
# Update makeblastdb and blastp for prokka
cd /opt/src
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install barrnap
# Install barrnap
cd /opt/src
cd /opt/src
...
@@ -73,7 +68,6 @@ From:python:3.7-stretch
...
@@ -73,7 +68,6 @@ From:python:3.7-stretch
/opt/src/prokka/bin/prokka --setupdb &&\
/opt/src/prokka/bin/prokka --setupdb &&\
ln -s /opt/src/prokka/bin/prokka /usr/local/bin
ln -s /opt/src/prokka/bin/prokka /usr/local/bin
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
cd /opt/src
cd /opt/src
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
...
@@ -141,7 +135,6 @@ From:python:3.7-stretch
...
@@ -141,7 +135,6 @@ From:python:3.7-stretch
cd /opt/src
cd /opt/src
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
cd /opt/src/pipeline_annotation
cd /opt/src/pipeline_annotation
git checkout dev &&\
./make
./make
...
...
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